Now you should run macro ReplaceMTEquations(*) which will place exported EPSs as linked files so you can place WORD document into InDesign document. Exported EPSs should be located in sub-folder "Equations" in folder where your WORD document is located. Now you can import your WORD document into InDesign and run script :)

(*)ReplaceMTEquations macro you can find in ZIPed archive with script - to add it to WORD you need to run WORD, press ALT+F11 (menu TOOLS -> MACRO -> VISUAL BASIC EDITOR), then go to the end of macros file (or press CTRL+End) and place contents of ReplaceMTEquations.txt file.